smftools 0.3.0

Single Molecule Footprinting Analysis in Python.

smftools

A Python tool for processing raw sequencing data derived from single molecule footprinting experiments into anndata objects. Additional functionality for preprocessing, spatial analyses, and HMM based feature annotation.

Philosophy

While genomic data structures (SAM/BAM) were built to handle low-coverage data (<1000X) along large references, smftools prioritizes high-coverage data (scalable to >1,000,000X coverage) of a few genomic loci at a time. This enables efficient data storage, rapid data operations, hierarchical metadata handling, seamless integration with various machine-learning packages, and ease of visualization. Furthermore, functionality is modularized, enabling analysis sessions to be saved, reloaded, and easily shared with collaborators. Analyses are centered around the anndata object, and are heavily inspired by the work conducted within the single-cell genomics community.

Dependencies

The following CLI tools need to be installed and configured before using the informatics (smftools.inform) module of smftools, which is used by the smftools load CLI command:

1. Dorado -> Basecalling, alignment, demultiplexing. Required for Nanopore SMF experiments, but not Illumina SMF experiments.
2. Minimap2 -> Aligner if not using dorado. Support for other aligners could eventually be added if needed.
3. Modkit -> Extracting read level methylation metrics from the MM/ML tags in BAM files. Only required for direct modification detection SMF protocols.